Using exome sequence data and Random Forest analysis to identify functional mutation signatures of 5 cancer differentiation subtypes. Russel Sutherland1, Salvador Diaz-Cano 2, Jane Moorhead2,, Richard J. Dobson3 1 Department
of Medical and Molecular Genetics, King’s College London, 8th Floor Tower Wing, Guy's Campus, London, SE1 9RT, UK 2Advanced Diagnostics, Histopathology, King’s College Hospital, Denmark Hill, SE5 9RS 3 NIHR Biomedical Research Centre for Mental Health South London and Maudsley NHS Foundation Trust & Institute of Psychiatry, Kings College London. Contacts:
[email protected]
Introduction The Pan-Cancer Analysis Project [1] aims to identify the genomic changes present in 12 different cancer types from the Cancer Genome Atlas (TCGA) set [2]. Cancer is a morphologically and genetically highly heterogeneous disease and as such we aimed to identify predictors of the 5 main differentiation subtypes in the Pan-Cancer Analysis [1] based on differences in their patterns of functional mutation. Whole exome sequencing was performed on tumour and normal tissue samples from 3129 patients enabling the identification of cancer related mutations in each patient. Clinical data were also collected for all patients, including gender and age. We used a Random Forest machine learning approach to compare the 5 differentiation subtypes in a pairwise fashion. Our presented results show that we were able to discriminate between Bladder Urotherial Cancer and Acute Myeloid Leukemia in unseen samples with 87.8% accuracy (95% CI : (78.71, 93.99)).
Analysis Pipeline and Methods Fisher’s exact test reduces gene 5x10 fold cross validation and list from 20775 to 𝑥 = 22. recursive feature elimination Random Forest
3129 samples
Tumour
Training urothelial squamous
Germline
Sequencing
Alignment
Variant Calling
Mutation Matrix
Sensitivity
20775 genes
Copyright © CancerHelp UK
Predictive Model
notmutated mutated 1343 423 142 178
Test
Specificity
► Data was retrieved from the Pan-Cancer Analysis repository (synapse accession: syn1710680) [1]. ► Functional somatic mutations unique to tumours were identified and represented as a samples x genes mutation matrix (mutated=1, non-mutated=0). ► Pairwise Random Forest models were built for the 5 cancer differentiation subtypes (Adenocarcinoma, Squamous, Urotherial, Brain, Haematological) ► Variable selection using Fisher’s Exact test was conducted on the training set to reduce the number of predictors. ► Further recursive feature selection was used in a 5x10 fold cross validation design. Random Forest models were based on the training set using the caret package in R [3]
► Predictive accuracy of each model was measured in an independent test set.
Urothelial vs Haematological Results
Specificity
0.77
Sensitivity
0.94
AUC
0.9677
MLL3, TTN, ARID1A, MLL2, FRG1B Sensitivity
Accuracy
Urothelial/ Haematological 0.878
► Genes included in the random forest model: ► MLL3 [4] is known to play a role in mixed lineage forms of Leukaemia. ► ARID1A [5,6] contributes to renal clear cell carcinoma and cervical cancer. Specificity
► TTN, although the largest gene, has been implicated in cancer by TCGA data [7].
Conclusions and further work ► We reduced 20775 binary predictors (genes) to 5 binary predictors of tumour class membership of Urotherial or Haematological subtypes. For space issues we only show Urothelial vs Haematological results. Average accuracy in the other comparisons is 85.0% ► Using a 5 variable random forest ensemble classification model we achieved near 90% accuracy in the task to distinguish between Acute Myeloid Leukaemia and Bladder Urothelial Cancer. ► This analysis may be clinically useful for the identification of the primary tumour type using exome sequence data from a secondary tumour. ► We now aim to produce a 5 class prediction model to assign test samples to one of the 5 differentiation subtype classes. We will use Random Forest and a k-medoids classifier. [1] Weinstein, J. N., et al. (2013). The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics 45(10) 1113-1120. [2] Muzny, D. M., et al. (2012). Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407) 330-337. [3] Kuhn, M. (2008). Building Predictive Models in R Using the caret Package. Journal of Statistical Software 28(5) 1-26. [5] Cho, H., et al. (2013). Loss of ARID1A/BAF250a expression is linked to tumor progression and adverse prognosis in cervical cancer. Human Pathology 44(7) 1365-1374. [4] Li, W. D., et al. (2013). Exome sequencing identifies an MLL3 gene germ line mutation in a pedigree of colorectal cancer and acute myeloid leukemia. Blood 121(8) 1478-1479. [6] Lichner, Z., et al. (2013). The Chromatin Remodeling Gene ARID1A Is a New Prognostic Marker in Clear Cell Renal Cell Carcinoma. American Journal of Pathology 182(4) 1163-1170. [7] Hofree, M., et al. (2013). Network-based stratification of tumor mutations. Nature Methods 10(11).
Financial Support by a BBSRC CASE Studentship in collaboration with Illumina Ltd (BB/I016287/1) is gratefully acknowledged.
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Kathrin Petra Aßhauer, Heiner Klingenberg, Robin Martinjak, Thomas Lingner and Peter Meinicke.
Department of Bioinformatics, Institute for Microbiology and Genetics, Georg-August University of Göttingen, Germany
Tools for fast and comparative metagenome analysis
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Alberto Benguría1, Francesca Finotello3, Sergio Callejas1, Rebeca Álvarez1, Fátima SánchezCabo2, Barbara di Camillo3, Concepción Hernández-Chico4 and Ana Dopazo1
1 Genomics Unit, 2 Bioinformatics Unit. Fundación Centro Nacional Investigaciones Cardiovasculares Carlos III (CNIC). c/ Melchor Fernández Almagro, 3. 28029 Madrid Spain. 3 Departament of Information Engineering. University of Padova, Padova, 35131 Italy. 4 Unidad de Genética Molecular, Hospital Universitario Ramón y Cajal, Ctra Colmenar km 9.1, 28034 Madrid, Spain.
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Erica Bianco1, Bruno Nevado2, Henry W. Soto3, Lourdes Vargas4 and Miguel Perez-Enciso5.
1 Universitat Autonoma de Barcelona - Centre de Recerca en Agrigenómica (CRAG) 2 Centre de Recerca en Agrigenómica (CRAG) 3 Universidad de Costa Rica 4 Sistema Nacional de Areas de Conservación (SINAC) 5 Universitat Autònoma de Barcelona (UAB) - Centre de Recerca en Agrigenòmica (CRAG) - Institut Català de Recerca i Estudis Avancats (ICREA)
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Alessandra Breschi, Silvia Pérez, Amaya Abad, Emilio Palumbo and Roderic Guigó.
Bioinformatics and Genomics Group, CRG, Center for Genomic Regulation and UPF, Barcelona, Spain
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Oriol Calvete1, Jose Reyes2, Sheila Zuñiga3, Socorro Rodriguez-Pinilla4, Victoria Fernandez1, Beatriz Paumard1 and Javier Benitez1.
1 Centro Nacional de Investigaciones Oncologicas (CNIO) 2 S. Digestivo, Hospital INCA 3 Bioinformática, Sistemas Genómicos 4 Servicio de anatomia patologica. FJD
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Angela Cánovas*, Oriol Canela±, Rayner González-Prendes*, Marcel Amills*, Raquel Quintanilla±
*Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain. ±Department of Animal Genetics, Center for Research & Technology, Food & Agriculture (IRTA), Torre Marimon, Caldes de Montbui, 08140 Spain.
Analyzing the muscle transcriptome of pigs with divergent lipid phenotypes through RNA-Seq
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Kuang-Lim Chan1, Eng-Ti Leslie Low1, Rozana Rosli1 and Mohd Firdaus Raih2.
1 Malaysian Palm Oil Board 2 Universiti Kebangsaan Malaysia
Identification of Oil Palm Genes via Gene Prediction and Transcriptome Sequencing
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E. Chernyaeva1,2, M. Rotkevich1, Dobrynin P.1, S. Simonov1, E. Shitikov3, D. Ischenko3, E. Ilina3, V. Zhuravlev2, M. Shulgina2, A. Lapidus1,4, S. J. O’Brien1
1 St. Petersburg State University, Dobzhansky Center for Genome Bioinformatics, Russia 2 St. Petersburg Phthisiopulmonology Institute, Russia 3 Research Institute of Physical and Chemical Medicine, Russia 4 St Petersburg Academic University, Russia
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Luca Cozzuto, Antonio Hermoso Pulido and Jean-François Taly.
CRG - Centre de Regulació Genòmica
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Fernando Cruz1, Federico Abascal2, Begoña Martínez-Cruz3, Miriam Rubio-Camarillo2, Sophia Derdak1, Tyler Alioto1, Alfonso Valencia2 and José A. Godoy3.
1Centre Nacional d'Anàlisi Genòmica, Barcelona, Spain. 2 Structural Biology and Biocomputing Programme, CNIO, Madrid, Spain 3 Dept. of Integrative Ecology (EBD-CSIC), Seville
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Joao Curado, Ionas Erb, Cedric Notredame and Roderic Guigo.
Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
How to correctly correlate NGS libraries: An example showing the effect of correlated histone modifications on alternative exon inclusion
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Johanna Christina Czeschik and Sven Rahmann.
University Duisburg-Essen
Differential use of the guilt-by-association principle for disease gene prioritization
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Javier Del Rey, Laia Ramos, Gemma Daina, Mariona Rius and Joaquima Navarro.
Unidad de Biología Celular y Genética Médica, Facultad de Medicina. Universidad Autónoma de Barcelona
Assessment of Whole Genome Amplification Systems for chromosomal alterations detection by NGS
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Paolo Di Tommaso, Maria Chatzou, Pablo Prieto and Cedric Notredame.
Centre for Genomic Regulation (CRG)
Nextlfow: a novel tool for high scalable computational pipelines
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Oliver Drechsel1, Luis Zapata1, Laia Bassaganyas Bars2, Rubayte Rahman1, Georgia Escaramis Babiano1, Xavier Estivill1 and Stephan Ossowski1.
1 Centre for Genomic Regulation (CRG) and UPF 2 University of California
Copy Number Variants in Chronic Lymphocytic Leukemia
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Andre Gohr1, Juliane C. Dohm1, Andre E. Minoche1 and Heinz Himmelbauer2.
1 Max Planck Institute for molecular genetics, Berlin, Germany 2 Centre for Genomic Regulation (CRG), Barcelona, Spain and Universitat Pompeu Fabra (UPF), Barcelona, Spain
Towards assembling heterozygous plant genomes
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1Center for Genomic Regulation (CRG), C. Dr. Aiguader, 88, 08003 Barcelona 2 Universitat Pompeu Fabra (UPF), C. Dr. Aiguader, 88, 08003 Barcelona
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Rayner Gonzalez-Prendes1, Angela Cánovas1, Arianna Manunza1, Sergi Beltrán2, Raul Tonda2, Raquel Quintanilla3 and Marcel Amills1.
1 Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain 2 Centre Nacional d'Anàlisi Genòmica, PCB, Barcelona, Spain 3 Genètica i Millora Animal, Lleida, 25198 Spain, IRTA
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Andreas Gruber, Manuel Belmadani and Mihaela Zavolan
University of Basel
3' end sequencing: no method to capture them all
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1 Centre for Genomic Regulation, Barcelona 2 Centro Nacional de Análisis Genómico, Barcelona 3 Department of Anatomic Pathology, Hospital Clínic, University of Barcelona, Institut d’Investigació Biomèdica August Pi i Sunyer (IDIBAPS), Barcelona 4 Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo
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Rohit Kolora1, Anne Weigert2, Michael Gerth2, Abdullah Sahyoun3, Peter Stadler4, Klaus Henle5, Rui Faria6, Christoph Bleidorn2, Katja Nowick3 and Martin Schlegel2
1 German Center for Integrative Biodiversity Research iDiv 2 Molecular Evolution & Animal Systematics, Institute of Biology, Universität Leipzig 3 Interdisciplinary Centre for Bioinformatics, Universität Leipzig 4 Institut für Informatik, Universität Leipzig 5 Helmholtz Centre for Environmental Research - UFZ 6 Centro de Investigação em Biodiversidade e Recursos Genéticos -CIBIO
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Manuel Landesfeind and Peter Meinicke.
Georg-August University of Göttingen, Germany
Predicting the functional repertoire of an organism from RNA-seq short reads alone
87
Jorge Langa1, Darrell Conklin1,2, Iratxe Montes1 and Andone Estonba1.
1 University of the Basque Country UPV/EHU 2 IKERBASQUE, Basque Foundation for Science
Quantitative approach to measure the transcriptome SNP density for European anchovy (Engraulis encrasicolus, L) and Atlantic mackerel (Scomber scombrus, L)
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1 Centro nacional de análisis genómico 2 Aix-Marseille University Medical School 3 Centro Nacional de Investigaciones Oncologicas 4 Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University 5 European Bioinformatics Institute, Hinxton, Cambridge
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Kean-Jin Lim, Tanja Paasela and Teemu H. Teeri
Department of Agricultural Sciences, University of Helsinki
Transcriptomics of Scots pine pinosylvin biosynthesis
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Ivan Limongelli1, Simone Marini2 and Riccardo Bellazzi2.
1 IRCCS Neurological Institute C. Mondino 2 University of Pavia
A novel algorithm to predict the deleteriousness of genomic coding variants
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Manfrini M 1,5, Barbanti-Bròdano G2, Mazzoni E1, Palatini J3, Warner S3, Tognon M1, Volinia S3,4, Croce CM3.
1 Department of Morphology, Surgery and Experimental Medicine, Experimental Biology Section, Ferrara University, Ferrara, Italy. 2 Spine Surgery, Istituto Ortopedico “Rizzoli”, Bologna, Italy. 3 Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH, USA. 4 Department of Morphology, Surgery and Experimental Medicine, Histology Section, Ferrara University, Ferrara, Italy. 5 Department of Information Engineering, Padova University, Padova, Italy.
microRNA Sequencing in Human Mesenchymal Stem Cell to Investigate Activated Regulative Network During Induced Osteogenesis.
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Santiago Marco Sola and Paolo Ribeca.
Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
Mapping in the era of third-generation sequencing technologies: GEM's stance
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Angelika Merkel, Anna Esteve, Emanuele Raineri and Simon Heath.
Centro Nacional de Análisis Genómico (CNAG)
Tissue- and Cell Type-specific DNA Methylation Profiles in Human Blood
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Andre E. Minoche1, Juliane C. Dohm1, Magda Montfort1, Thomas Hackl2 and Heinz Himmelbauer1.
1 Centre for Genomic Regulation (CRG) 2 Biocenter, University Würzburg, Germany
Validation of gene models using PacBio SMRT sequences
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A.Mitra1, M.Skrzypczak2, K.Ginalski2 & M.Rowicka1
1 Institute for Translational Sciences, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX, 77555, USA. 2 Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
Strategies for sequencing low diversity samples and achieving ultimate sequencing accuracy using Illumina platform
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Michael Moffat.
MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, UK
The polycomb deficient DNA methylome
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Mola-Caminal Marina1, Rabionet Raquel 2, Soriano-Tárraga Carolina 1, Giralt-Steinhauer Eva 1 , Carrera Caty 3, Susak Hana 2, Ossowski Stephan 2, Fernández-Cadenas Israel 4, Estivill Xavier 2, Roquer Jaume 1, Jiménez-Conde Jordi 1
1 Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar, Barcelona, Spain 2 Bioinformatics and Genomics, CRG, Barcelona, Spain 3 Neurovascular Research Lab, Vall d’Hebron Research Institute, Barcelona, Spain 4 Fundació Docència i Recerca Mútua Terrassa, Barcelona, Spain
Identification of genes involved in Functional Outcome and Disability after Ischemic Stroke through Exome Sequencing of extreme phenotypes
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Iratxe Montes1, Darrell Conklin2, Jorge Langa1 and Andone Estonba1.
1 University of the Basque Country UPV/EHU 2 University of the Basque Country UPV/EHU; IKERBASQUE Basque Foundation for Science
SNP discovery by high-throughput sequencing in the Atlantic mackerel (Scomber scombrus, L) transcriptome
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Maria Murgarella1, André Corvelo2, Tyler Alioto2, Beatriz Novoa3, Antonio Figueras3, David Posada1 and Carlos Canchaya1.
1 Universidade de Vigo 2 Centre Nacional d’Anàlisi Genòmica (CNAG) 3 Instituto de Investigaciones Marinas (IIM) - Consejo Superior de Investigaciones Científicas (CSIC)
Reducing fragmentation of genome assembly in Mytilus galloprovincialis by using a hierarchical sequencing strategy
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Alinda Nagy and László Patthy.
Institue of Enzymology, Research Centre for Natural Scienes, Hungarian Academy of Sciences
FixPred: Correction of erroneous protein sequences in public databases
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Gemma Navarro, Raquel Longarón, Sonia Servitja, Luz Martínez-Avilés, Marta Castells, Ignacio Tusquets and Beatriz Bellosillo.
Hospital del Mar
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Preethy Sasidharan Nair1, Tuire Kuusi2, Minna Ahvenainen1, Harri Lähdesmäki3 and Irma Järvelä1.
1 Department of Medical Genetics, Haartman Institute, University of Helsinki, P.O. Box 720, 00014 University of Helsinki, Finland 2 DocMus Department, Sibelius Academy, University of the Arts Helsinki, P.O. Box 86, 00251 Helsinki, Finland 3 Department of Information and Computer Science, Aalto University, FI-00076 Aalto, Finland
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1 Department of Microbiology, University of Washington, Seattle 98109, USA; 2 Washington National Primate Research Center, Seattle 98109, USA; 3 BGI-Shenzhen, Shenzhen 518083, China; 4 BGI-Guangzhou, Guangzhou 511400, China
Deep sequencing of HIV infected cells: insights into nascent transcription and host-directed therapy
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Ernesto Picardi1,2,3 and Graziano Pesole1,2,3,4
1Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy 2Institute of Biomembranes and Bioenergetics (IBBE), CNR, Bari, Italy 3National Institute of Biostructures and Biosystems (INBB), Rome, Italy 4Center of Excellence in Genomics (CEGBA), Bari, Italy
Investigating the eukaryotic inosinome through the REDItools package
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Alessandro Pietrelli1 , Chiara Di Resta2, Simone Sala3, Paolo Della Bella3, Gianluca De Bellis1, Maurizio Ferrari2,5, Roberta Bordoni1 and Sara Benedetti4
1 Institute of biomedical technologies, National Council of Resarch (ITB-CNR), Milan; 2 Vita-Salute San Raffaele University, Milan; 3 Department of arrhythmology, San Raffaele Hospital, Milan; 4 Laboratory of Clinical Molecular Biology, Diagnostica e Ricerca San Raffaele, Milan; 5 Genomic Unit for the Diagnosis of Human Pathologies, Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
Identification of candidate genes for Brugada Syndrome by targeted next generation sequencing
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Niko Popitsch, Philipp Rescheneder and Miguel Gallach.
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030 Vienna, Austria
Intragenomic Sequence Similarity Patterns assist in de novo Genome Annotation
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M. Rayko1, E. Chernyaeva1, A. Tkachenko2 and S. J. O’Brien1.
1 St. Petersburg State University, Dobzhansky Center for Genome Bioinformatics, Russia 2 St. Petersburg State University, Department of Microbiology, Russia
Whole genome sequence of the cellulose-synthesizing bacteria Gluconacetobacter rhaeticus and evaluation of the four bacterial genome assemblers
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Ettore Rizzo1, Jared B. Hawkins2, Yassine Souilmi3, Peter Tonellato2, Dennis P. Wall4 and Riccardo Bellazzi1.
1 University of Pavia 2 Harvard Medical School, Boston, MA 3 Faculty of Sciences of Rabat, Morocco 4 Stanford Medical School, Palo Alto, CA
COSMOS: a workflow management system for NGS Analysis in the Cloud
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Bernardo Rodríguez1,2, Emilio Palumbo1,2, Paolo Ribeca3, Alessandra Breschi1, Dmitri D. Pervouchine1, Thomas R. Gingeras4, Roderic Guigó1,2, and Sarah Djebali1,2,
1 Centre for Genomic Regulation, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain. 2 Universitat Pompeu Fabra (UPF), Barcelona, Spain 3 CNAG, Barcelona, Spain 4 Cold Spring Harbour Laboratory
ChimPipe: a flexible pipeline for the detection of chimeras from RNA-seq data
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Simone Röh1, Peter Weber1, Monika RexHaffner1, Kristina B Mercer2, Bekh Bradley2, Kerry J Ressler2, Elisabeth B Binder1 and Torsten Klengel1.
1 Department of Translational Research, Max Planck Institute of Psychiatry 2 Department of Psychiatry and Behavioral Sciences, Emory School of Medicine
Reduced PTSD risk is conferred by a structural variation observed in an NGS screening approach
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Zachary Romer1, Siobhan Watkins2, Catherine Putonti1,2,3
Departments of 1Computer Science, 2Biology, and 3Bioinformatics Loyola University Chicago, Chicago, IL USA
Moving into Uncharted Waters: An Investigation into Complex Aquatic Phage Communities
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Miriam Rubio-Camarillo, Gonzalo Gómez-López, Jose María Fernandez, Alfonso Valencia and David Gonzalez-Pisano
CNIO
RUbioSeq: a suite of parallelized pipelines to automate NGS analyses
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A.Rueda1, J.P.Florido1, F.J.López-Domingo1, J.Dopazo1,2,3, J.Santoyo-López1
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ngsCAT: a next generation sequencing Capture Assessment Tool
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Gabriella Rustici and Sarah L. Morgan.
EMBL-European Bioinformatics Institute
Impact and sustainability of hands-on training in the analysis of next-generation sequencing data
64
Ester Saus1,2, Leszek P. Pryszcz1,2, Damian Loska1,2, Jose L Rodriguez-Ales1,2, Heinz Himmelbauer1,2, Toni Gabaldón1,2,3.
1 Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG). Dr. Aiguader, 88. 08003 Barcelona, Spain 2 Universitat Pompeu Fabra (UPF). 08003 Barcelona, Spain. 3 Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
High-throughput RNA structure probing using Illumina sequencing technology
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Melanie Schirmer1, Umer Z. Ijaz1, Linda D’Amore2, Neil Hall2, William T. Sloan1, Christoper Quince1
1 Water Research Group, University of Glasgow, G12 8LT, United Kingdom 2 Institute of Integrative Biology, University of Liverpool, L69 7ZB, UK
Validation of State of the Art Library Preparation Methods for Illumina Amplicon Sequencing
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Ronald Schuyler, Angelika Merkel, Emanuele Raineri and Simon Heath.
Centro Nacional de Análisis Genómico
Periodic DNA Methylation Patterns are Established During Lymphocyte Differentiation
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Hyunjin Shin, David Merberg, Sunita Badola, Matthew Schu, Bin Li, Andrew Krueger, William Trepicchio, Jeffrey Ecsedy and Huifeng Niu.
Department of Translational Medicine, Takeda Pharmaceuticals International Co. Cambridge, MA 02139, U.S.A.
The genomic characterization of five solid tumor types revealed by whole exome sequencing
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Yoram Shotland.
Chemical Engineering, Shamoon College of Engineering
The draft genome of Leptolyngbya sp. a highly abundant cyanobacteria in biological desert crust, shade lights on possible clues to bacterial dehydration resistant
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Daniel Silberschmidt and Ana Vivancos.
Vall d'Hebron Institute of Oncology, Barcelona
One-step alignment pipeline to purge fastq files from heterospecies contaminating reads.
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Victor Solovyev1, Igor Seledtsov2, Vladimir Molodtsov2, Denis Vorobyev2 and Oleg Fokin2.
1 King Abdullah University of Science and Technology 2 Softberry Inc.
Improved algorithms for next generation data processing
97
Rory Stark and Thomas Carroll
University of Cambridge, Cancer Research UK, Cambridge Institute
ChIPQC: Computing and reporting quality metrics for assessing ChIP-seq experiments
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Hana Susak, Luis Zapata, Oliver Drechsel, Rubayte Rahman and Stephan Ossowski.
Centre for Genomic Regulation (CRG)
Tumor heterogeneity in Chronic Lymphocytic Leukemia
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Russel Sutherland1, Salvador Diaz-Cano2, Jane Moorhead2 and Richard Dobson3.
1 King's College London 2 King’s College Hospital NHS Foundation Trust 3 NIHR Biomedical Research Centre for Mental Health South London and Maudsley NHS Foundation Trust & Institute of Psychiatry
Using exome sequence data and Random Forest analysis to identify functional mutation signatures of 5 cancer differentiation subtypes.
35
Electra Tapanari1, Julien Lagarde2, Javier Santoyo-Lopez3, Jose Manuel Gonzalez1, Barbara Uszczyńska2, Anne-Maud Ferreira4, Alexandre Reymond4, Jennifer Harrow1 and Roderic Guigó2.
1 Wellcome Trust Sanger Institute 2 Centre de Regulació Genòmica (CRG) 3 Genomics & Bioinformatics Platform of Andalusia (GBPA) 4 The University of Lausanne
Examining tissue specific RACEseq extension of lncRNAs in the Human GENCODE gene set
2
Tatiana Tatarinova1, Alona Kryshchenko1, Martin Triska1,2, Mehedi Hassan2, Denis Murphy2, Michael Neely1 and Alan Schumitzky1
1 Children’s Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA 2 Genomics and Computational Biology research group, University of South Wales, Treforest, Wales, UK
NPEST: a nonparametric method and a database for transcription start site prediction
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Svitlana Tyekucheva, Michaela Bowden, Giorgia Zadra, Mark Pomerantz, Matthew Freedman and Massimo Loda.
Dana-Farber Cancer Institute
Methods for RNA-Seq profiling of formalin fixed paraffin embedded prostate cancer samples
99
Peter Vegh1, David Magee2, Nicolas Nalpas2, Kenneth Bryan3, Matthew S. McCabe3, John Browne2, Kevin Conlon4, Stephen Gordon4, Daniel G. Bradley5, David MacHugh2 and David J. Lynn1
1 Animal & Bioscience Research Department, AGRIC, Teagasc, and Smurfit Institute of Genetics, Trinity College Dublin 2 Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Agriculture, Food Science and Veterinary Medicine, University College Dublin 3 Animal & Bioscience Research Department, AGRIC, Teagasc 4 School of Veterinary Medicine, University College Dublin 5 Molecular Population Genetics, Smurfit Institute of Genetics, Trinity College Dublin
MicroRNA regulation of the bovine alveolar macrophage response to Mycobacterium bovis
43
Thomas Wolf1, Jan Budczies2, Stephan Gade3, Sibylle Loibl3, Gunter von Minckwitz3, Carsten Denkert2 and Wilko Weichert1.
1 German Consortium for Translational Cancer Research (DKTK) / Institute for Pathology, University Hospital Heidelberg 2 Institute for Pathology, Charité University Hospital Berlin / German Consortium for Translational Cancer Research (DKTK) 3 German Breast Group (GBG)
Computational Approaches to Panel Sequencing : Obstacles and Perspectives in Translating a Marker Panel to the Clinic
98
Yayoi Natsume-Kitatani1 and Hiroshi Mamitsuka2
1 JST, PRESTO 2 Kyoto University
Detection of histone modification dynamics at Ash1 target genes
65
Feng Yue1, Yin Shen2, Samantha Kuan2, Zhen Ye2, Mike Beer3 and Bing Ren2.
1 Penn State University 2 Ludwig Institute for Cancer Research, UCSD School of Medicine 3 Johns Hopkins University School of Medicine, Dept. of Biomedical Engineering and McKusick-Nathans Institute of Genetic Medicine
A comparative analysis of the cis-regulatory landscape in the mouse genome
